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Receptor
PDB id Resolution Class Description Source Keywords
3JYN 2.01 Å EC: 1.6.5.5 CRYSTAL STRUCTURES OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000 QUINONE OXIDOREDUCTASE COMPLEXED WITH NADPH PSEUDOMONAS SYRINGAE PV. TOMATO ROSSMANN FOLD PROTEIN-NADPH COMPLEX OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURES OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000 QUINONE OXIDOREDUCTASE AND ITS COMPLEX WITH NADPH BIOCHEM.BIOPHYS.RES.COMMUN. V. 390 597 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NDP A:350;
Valid;
none;
submit data
745.421 C21 H30 N7 O17 P3 c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3JYN 2.01 Å EC: 1.6.5.5 CRYSTAL STRUCTURES OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000 QUINONE OXIDOREDUCTASE COMPLEXED WITH NADPH PSEUDOMONAS SYRINGAE PV. TOMATO ROSSMANN FOLD PROTEIN-NADPH COMPLEX OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURES OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000 QUINONE OXIDOREDUCTASE AND ITS COMPLEX WITH NADPH BIOCHEM.BIOPHYS.RES.COMMUN. V. 390 597 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3JYN - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 280 families.
1 3JYN - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 1QOR - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 187 families.
1 3JYN - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 4RVU - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
3 3QWB - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
4 1QOR - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NDP; Similar ligands found: 172
No: Ligand ECFP6 Tc MDL keys Tc
1 NDP 1 1
2 0WD 0.827273 1
3 NAI 0.803738 0.986842
4 NMN AMP PO4 0.794643 0.948052
5 NPW 0.692308 0.962025
6 NZQ 0.686441 0.987013
7 1DG 0.68 1
8 DG1 0.68 1
9 A2R 0.650943 0.909091
10 A22 0.64486 0.934211
11 TXP 0.644628 0.924051
12 ATR 0.640777 0.894737
13 NA7 0.636364 0.886076
14 XNP 0.620968 0.949367
15 AP0 0.598361 0.948718
16 A2P 0.598039 0.881579
17 NJP 0.574803 0.923077
18 25L 0.550847 0.934211
19 ODP 0.550388 0.936709
20 NAX 0.544 0.949367
21 25A 0.53913 0.921053
22 80F 0.537879 0.914634
23 2AM 0.529412 0.87013
24 6V0 0.519685 0.974026
25 NAP 0.514493 0.922078
26 7L1 0.507143 0.763441
27 EAD 0.507143 0.949367
28 A2D 0.504673 0.921053
29 TXE 0.503876 0.935897
30 NA0 0.496454 0.910256
31 TXD 0.496124 0.911392
32 SAP 0.495575 0.875
33 AGS 0.495575 0.875
34 P1H 0.493056 0.925926
35 CO7 0.489796 0.791209
36 TAP 0.489362 0.864198
37 PAP 0.482456 0.907895
38 BA3 0.481818 0.921053
39 NAJ PZO 0.478261 0.924051
40 ATP 0.477876 0.921053
41 HEJ 0.477876 0.921053
42 B4P 0.477477 0.921053
43 AP5 0.477477 0.921053
44 ADP 0.477477 0.921053
45 OAD 0.47541 0.897436
46 AR6 0.473684 0.896104
47 AQP 0.473684 0.921053
48 5FA 0.473684 0.921053
49 APR 0.473684 0.896104
50 AN2 0.473214 0.909091
51 3OD 0.467742 0.897436
52 50T 0.464912 0.884615
53 NAJ PYZ 0.464789 0.879518
54 9X8 0.463415 0.851852
55 PO4 PO4 A A A A PO4 0.463415 0.857143
56 V3L 0.461538 0.896104
57 2A5 0.46087 0.85
58 AT4 0.460177 0.886076
59 A1R 0.459016 0.841463
60 4AD 0.459016 0.875
61 ADQ 0.459016 0.897436
62 OVE 0.458716 0.8375
63 OMR 0.458647 0.813953
64 PPS 0.457627 0.811765
65 AD9 0.456897 0.897436
66 CA0 0.45614 0.897436
67 M33 0.45614 0.884615
68 ADJ 0.455882 0.879518
69 A3P 0.455357 0.894737
70 ACP 0.452174 0.897436
71 ENP 0.451613 0.85
72 UP5 0.451128 0.948052
73 SRP 0.45 0.8625
74 ANP 0.449153 0.897436
75 ACQ 0.449153 0.897436
76 PRX 0.448276 0.82716
77 A3R 0.447154 0.841463
78 5AL 0.445378 0.884615
79 7D4 0.443478 0.8375
80 ADX 0.443478 0.811765
81 6YZ 0.438017 0.897436
82 A 0.436364 0.894737
83 AMP 0.436364 0.894737
84 4TC 0.433824 0.924051
85 7D3 0.433628 0.8375
86 DCA 0.433566 0.788889
87 ETB 0.433566 0.797753
88 BIS 0.433071 0.864198
89 1ZZ 0.433071 0.802326
90 00A 0.432 0.864198
91 ATF 0.429752 0.886076
92 DQV 0.428571 0.934211
93 0T1 0.427586 0.788889
94 5SV 0.427419 0.788235
95 8QN 0.427419 0.884615
96 3AM 0.427273 0.857143
97 N01 0.426573 0.884615
98 PR8 0.425197 0.811765
99 LAD 0.425197 0.821429
100 WAQ 0.425197 0.841463
101 DTP 0.425 0.8375
102 AMO 0.424 0.886076
103 PAJ 0.424 0.843373
104 APC 0.423729 0.886076
105 UPA 0.423358 0.935897
106 48N 0.422222 0.853659
107 FYA 0.421875 0.860759
108 PTJ 0.421875 0.853659
109 CNA 0.421429 0.910256
110 PUA 0.42069 0.9125
111 DND 0.419118 0.910256
112 NXX 0.419118 0.910256
113 AV2 0.418033 0.848101
114 COA 0.417808 0.788889
115 3UK 0.417323 0.897436
116 OOB 0.416 0.909091
117 IVC 0.415584 0.78022
118 DAT 0.415254 0.8375
119 NDO 0.414966 0.897436
120 139 0.414286 0.901235
121 B5V 0.414062 0.886076
122 T99 0.413223 0.886076
123 TAT 0.413223 0.886076
124 3AT 0.413223 0.896104
125 YLB 0.413043 0.784091
126 62F 0.4125 0.823529
127 ABM 0.412281 0.848101
128 B5M 0.412214 0.875
129 YAP 0.412214 0.875
130 YLP 0.411765 0.784091
131 NB8 0.410853 0.853659
132 ME8 0.410853 0.802326
133 SON 0.410256 0.886076
134 DLL 0.409449 0.909091
135 AHX 0.409449 0.853659
136 CAO 0.409396 0.763441
137 30N 0.409396 0.72449
138 AMX 0.409396 0.797753
139 COS 0.409396 0.771739
140 7D5 0.409091 0.8125
141 4UW 0.408759 0.9125
142 F2R 0.408451 0.825581
143 APX 0.407692 0.841463
144 SRA 0.40708 0.85
145 CMX 0.406667 0.788889
146 SCO 0.406667 0.788889
147 TYM 0.405797 0.886076
148 COD 0.405594 0.777778
149 CA6 0.405229 0.70297
150 OXK 0.405229 0.771739
151 AP2 0.405172 0.886076
152 A12 0.405172 0.886076
153 9SN 0.40458 0.853659
154 LAQ 0.404412 0.802326
155 T5A 0.404255 0.914634
156 FAM 0.403974 0.771739
157 ACO 0.403974 0.763441
158 FCX 0.403974 0.763441
159 VO4 ADP 0.403226 0.860759
160 ADP VO4 0.403226 0.860759
161 YLC 0.402878 0.823529
162 1VU 0.402597 0.763441
163 B5Y 0.401515 0.875
164 FA5 0.401515 0.886076
165 HAX 0.401316 0.771739
166 AR6 AR6 0.4 0.871795
167 CAJ 0.4 0.771739
168 AFH 0.4 0.843373
169 APU 0.4 0.923077
170 A U 0.4 0.898734
171 TXA 0.4 0.886076
172 4UU 0.4 0.948052
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3JYN; Ligand: NDP; Similar sites found with APoc: 254
This union binding pocket(no: 1) in the query (biounit: 3jyn.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
1 1SQL GUN None
2 5C2N NAG None
3 5GZ6 NDP 1.23077
4 5GZ6 7C3 1.23077
5 1CER NAD 1.53846
6 5UR0 NAD 1.53846
7 2O4C NAD 1.53846
8 5N6C NAD 1.66667
9 1YS4 NAP 1.84615
10 4Z0H NAD 1.84615
11 2D2I NAP 1.84615
12 2CDC XYP 1.84615
13 2CDC NAP 1.84615
14 3B20 NAD 1.84615
15 2CDC XYS 1.84615
16 3WBF NAP 1.96721
17 3WBF API 1.96721
18 6FC1 MGP 2.07254
19 1DSS NAD 2.15385
20 1E5Q NDP 2.15385
21 4HDK 13X 2.15385
22 5N9X THR 2.15385
23 1J49 NAD 2.15385
24 1F06 2NP 2.1875
25 1F06 NDP 2.1875
26 5KZD RCJ 2.38908
27 3B1F NAD 2.41379
28 1RM4 NDP 2.46154
29 2I3G NAP 2.46154
30 1TL2 NDG 2.54237
31 5N2I NAP 2.58621
32 4J4H NAI 2.7027
33 4J4H 1J1 2.7027
34 4JK3 NAD 2.7027
35 3HGM ATP 2.72109
36 4JGP PYR 2.76498
37 4C2C ALA ALA ALA 2.76923
38 1X7D NAD 2.76923
39 1X7D ORN 2.76923
40 1GR0 NAD 2.76923
41 6GZD LCI 2.76923
42 1GZ4 ATP 2.76923
43 2GSD NAD 2.76923
44 1DCP HBI 2.88462
45 1DRV A3D 2.9304
46 5FII PHE 2.94118
47 3OND NAD 3.07692
48 3OND ADN 3.07692
49 1O0S NAI 3.07692
50 1U8X NAD 3.07692
51 6F3N ADN 3.07692
52 6F3N NAD 3.07692
53 6F3M NAD 3.07692
54 3CMC NAD 3.07692
55 5BXV MGP 3.125
56 6HKE MLT 3.14465
57 2XKO AKG 3.15315
58 5TC4 NAD 3.16456
59 1M0U GSH 3.21285
60 5NM7 GLY 3.38346
61 5M67 NAD 3.38462
62 5M67 ADE 3.38462
63 5M67 3D1 3.38462
64 5Z20 NAI 3.38462
65 5NUE NAD 3.38462
66 4PLT NAI 3.38462
67 4PLT OXM 3.38462
68 5NUF NAD 3.38462
69 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 3.40136
70 2A92 NAI 3.42679
71 2YLN CYS 3.53357
72 3BAZ NAP 3.6036
73 2WPB ZZI 3.61842
74 1O6Z NAD 3.63036
75 2HK9 NAP 3.63636
76 2ZJ1 ARJ 3.69231
77 2ZJ1 NAD 3.69231
78 2HZL PYR 3.69231
79 3H5N ATP 3.69231
80 1EBF NAD 3.69231
81 5A1S FLC 3.69231
82 1X8X TYR 3.72671
83 1JAY NAP 3.77358
84 1NCE CB3 3.78788
85 4XMF HSM 3.80435
86 3ABI NAD 4
87 2GCG NDP 4
88 3EF0 ALF 4
89 1GAD NAD 4
90 1KC7 PPR 4
91 4E5N NAD 4
92 5AX9 4KT 4.22078
93 1DIG NAP 4.24837
94 5MDH NAD 4.30769
95 3NJ4 AFX 4.30769
96 3NJ4 NAD 4.30769
97 4MDH NAD 4.30769
98 4XDY NAI 4.30769
99 5OJL TXP 4.36242
100 1VM6 NAD 4.38596
101 2DTJ THR 4.49438
102 3LA3 2FT 4.52675
103 1HKU NAD 4.61538
104 3CIF NAD 4.61538
105 3V1Y NAD 4.61538
106 2Z49 AMG 4.61538
107 5WHU SIA GAL GLC 4.69799
108 3NGL NAP 4.71014
109 2DT5 NAD 4.73934
110 3B9O FMN 4.92308
111 5Z21 NAI 4.92308
112 4MP8 MLI 4.92308
113 4MP8 NAD 4.92308
114 4YMJ 4EJ 4.93421
115 4S1D 41M 5
116 3NFD COA 5.22876
117 5L95 AMP 5.23077
118 1B8U NAD 5.23077
119 3H9E NAD 5.23077
120 2B5W NAP 5.23077
121 2B4R AES 5.23077
122 2B4R NAD 5.23077
123 6BII NAP 5.53846
124 2VYN NAD 5.53846
125 2GZ3 NAP 5.53846
126 5EIN NAP 5.53846
127 2VHW NAI 5.53846
128 4LH7 1X8 5.57276
129 2Z77 NCA 5.7554
130 3KB6 NAD 5.84615
131 5AOV NAP 5.84615
132 2DBZ NAP 5.84615
133 2UVO NDG 5.84795
134 2UVO NAG 5.84795
135 1VBO MAN MAN MAN 6.04027
136 5EES NAP 6.07287
137 4ZJS 4P0 6.08696
138 1M1B SPV 6.1017
139 1NVM NAD 6.15385
140 3KIH GDL 6.18557
141 1BXG NAD 6.46154
142 1C1X NAD 6.46154
143 5TE1 7A2 6.46154
144 5D3U TRP 6.46154
145 1BW9 NAD 6.46154
146 5YU3 NAD 6.76923
147 5YU3 PRO 6.76923
148 6C4N NAP 6.76923
149 3B6R CRN 6.76923
150 1HYH NAD 6.79612
151 1V8B NAD 7.07692
152 3QV1 NAD 7.31707
153 4L8F MTX 7.37179
154 3UKR CKH 7.38462
155 3I9U DTU 7.60456
156 3HYW DCQ 7.69231
157 1N4K I3P 7.69231
158 6C92 EGV 7.69231
159 1EXF GLY 7.85124
160 4DDY DN6 7.98479
161 1SQK LAR 8
162 5TG5 JW8 8.16327
163 1ZOS MTM 8.26087
164 5H81 NAP 8.30769
165 4DPL NAP 8.30769
166 1OMO NAD 8.38509
167 4ZGS NAD 8.61539
168 1RM0 D6P 8.61539
169 5ZZ6 ADP 8.65385
170 5ZZ6 NAD 8.65385
171 1LUA NAP 8.7108
172 2JL1 NAP 8.7108
173 2FMD MAN MAN 8.75
174 4BVA NDP 8.92308
175 3AB4 THR 8.92308
176 4USI AKG 9.09091
177 5A1T NAI 9.09091
178 5A1T OXM 9.09091
179 1NVT NAP 9.23077
180 1GV0 NAD 9.67742
181 1EZ4 NAD 9.74843
182 1LSS NAD 10
183 5YEC ATP 10.084
184 2CVQ NDP 10.0917
185 1TE2 PGA 10.177
186 5NE2 DGL 10.4317
187 1QAW TRP 10.8108
188 1GUZ NAD 10.9677
189 1P0F NAP 11.0769
190 2OOR NAD 11.0769
191 1NYT NAP 11.8081
192 1P77 ATR 12.1324
193 4GKY MAN 12.2605
194 3ZZQ TRP 12.3077
195 1CDO NAD 12.6154
196 1WP4 NDP 13.1488
197 2JHF NAD 13.2308
198 4RQU NAD 13.8462
199 1KOL NAD 14.3216
200 2X2M X2M 14.3312
201 1XX4 BAM 14.9425
202 2ZB3 NDP 16.3077
203 4RDH AMP 16.3194
204 1OCU PIB 16.6667
205 5N17 8FK 16.6667
206 4JCA CIT 16.7665
207 4D79 ATP 17.029
208 1SC6 NAD 17.2308
209 5YEE LAB 17.6471
210 2DM6 NAP 17.8462
211 2DM6 IMN 17.8462
212 5ZZA LAB 19.8347
213 5FI3 NAP 20.6154
214 43CA NPO 23.0089
215 5VKT NAP 23.0769
216 1YQD NAP 24.3077
217 2Y69 CHD 25.3968
218 1N9G NAP 25.5385
219 4WAS COO 25.5385
220 4WAS NAP 25.5385
221 1KEV NDP 26.1538
222 1F8F NAD 27.0769
223 4B7X NAP 27.3846
224 3B6Z CO7 27.3846
225 2ZB4 NAP 28
226 2ZB4 5OP 28
227 4GKV NAD 28.2738
228 3TWO NDP 29.2308
229 1PL6 NAD 29.8462
230 1E3I CXF 29.8462
231 1PL6 572 29.8462
232 1D1T NAD 30.1538
233 1LLU NAD 30.4615
234 1U3U NAD 30.4615
235 1U3U BNF 30.4615
236 2FZW NAD 31.3846
237 1YKF NAP 31.3846
238 4Y1B NAP 33.8462
239 3WLE NAD 33.8462
240 5W97 CHD 34.0426
241 2J8Z NAP 35.0769
242 1R37 NAD 35.3846
243 5DOZ NDP 35.6923
244 3GFB NAD 39.6923
245 4W6Z 8ID 40
246 2DFV NAD 40.6154
247 4JBI NDP 40.9231
248 4A0S NAP 41.8462
249 1H2B NAJ 42.4615
250 4IDC NDP 43.6923
251 4IDC 1XX 43.6923
252 5DP2 NAP 44.6154
253 5O9F NAD 44.9231
254 5O9F 9ON 44.9231
Pocket No.: 2; Query (leader) PDB : 3JYN; Ligand: NDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3jyn.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
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